Philippe Dugourd - Academia.edu (original) (raw)
Papers by Philippe Dugourd
Structural Dynamics, 2020
A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a serie... more A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a series of poly-peptide radical cations containing both histidine and tryptophan. The proton transfer is driven by the gas-phase basicity difference between residues. The fragmentation scheme indicates that the gas-phase basicity of histidine is lower than that of radical tryptophan so that histidine is always pulling the proton away from tryptophan. However, the proton transfer requires the two basic sites to be in close proximity, which is rate limited by the peptide conformational dynamics. PT rate measurements were used to probe and explore the peptide conformational dynamics in several poly-glycines/prolines/alanines. For small and unstructured peptides, the PT rate decreases with the size, as expected from a statistical point of view in a flat conformational space. Conversely, if structured conformations are accessible, the structural flexibility of the peptide is decreased. This slows d...
Journal of the American Chemical Society, 2003
Amino acids exist as zwitterions in solution and in their canonical forms in the gas phase. 1-5 T... more Amino acids exist as zwitterions in solution and in their canonical forms in the gas phase. 1-5 The zwitterionic form can be stabilized in the gas phase by salt bridge interactions when a net charge is present, 6,7 or by shielding of the charges, either by the addition of water molecules 8,9 or by complex formation. 10 Calculations suggest that two water molecules are sufficient to stabilize a zwitterion in glycine, 11 the simplest amino acid. In peptides, the charge shielding function can be accomplished through self-solvation. At present, there is very little information available about the minimum peptide size required to stabilize a zwitterion, 12-14 and what information is available has been obtained on charged peptides using indirect methods. Here, we report studies of zwitterion formation in small neutral alanine-based peptides using, for the first time, a direct probe of the charge distribution. We have used molecular beam electric deflection measurements to determine the electric dipole susceptibility of unsolvated WA n and Ac-WA n-NH 2 (W) tryptophan and A) alanine) peptides with up to five alanines (the capped Ac-WA n-NH 2 peptides cannot form zwitterions). We find that the WA n peptides remain in the canonical form at room temperature. The measurements were performed on an apparatus consisting of a matrix-assisted laser desorption (MALD) source coupled to an electric beam deflection setup with a position-sensitive timeof-flight mass spectrometer. 15 The peptides were synthesized using FastMoc chemistry with an Applied Biosystems model 433A peptide synthesizer. MALD targets were prepared by pressing a 1:3 ratio of the peptide and high purity cellulose powder. Peptides were desorbed from the target with the third harmonic of a pulsed Nd:YAG laser (355 nm) into a helium flow generated with a piezoelectric valve that is synchronized with the desorption laser. A molecular beam leaves the source through a 5 cm long nozzle. Both ions and neutrals are produced in the desorption step. The ions are ejected from the beam with a transverse electric field, and the resulting neutral beam is tightly collimated by two slits before it travels through the 15 cm long electric deflector. The deflector provides both an electric field F (F) 0 to 2 × 10 7 V m-1) and a field gradient ∂F/∂z. The direction of the field, z, and its gradient are perpendicular to the beam axis. One meter after the deflector, the peptides are photoionized with the fourth harmonic of a Nd: YAG laser (266 nm) in the extraction region of a position-sensitive time-of-flight mass spectrometer. The velocity of the peptides in the neutral beam is selected and measured with a mechanical chopper that is synchronized with the ionization laser. The beam profile of rigid molecules is symmetrically broadened in the deflector, while for nonrigid molecules (i.e., when one cannot separate the vibrational and rotational Hamiltonians such as for those molecules studied here), the beam is globally deflected toward the high field. 16 The deflection:
The Journal of Physical Chemistry A, 2017
Journal of the American Society for Mass Spectrometry, 2018
The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage in... more The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are f...
Journal of the American Society for Mass Spectrometry, 2017
The visible photodissociation mechanisms of QSY7-tagged peptides of increasing size have been inv... more The visible photodissociation mechanisms of QSY7-tagged peptides of increasing size have been investigated by coupling a mass spectrometer and an optical parametric oscillator laser beam. The experiments herein consist of energy resolved collision-and laser-induced dissociation measurements on the chromophore-tagged peptides. The results show that fragmentation occurs by similar channels in both activation methods, but that the branching ratios are vastly different. Observation of a size-dependent minimum laser pulse energy required to induce fragmentation, and collisional cooling rates in time resolved experiments show that laser-induced dissociation occurs through the absorption of multiple photons by the chromophore and the subsequent heating through vibrational energy redistribution. The differences in branching ratio between collision-and laser-induced dissociation can then be understood by the highly anisotropic energy distribution following absorption of a photon.
Journal of the American Society for Mass Spectrometry, Jan 9, 2016
Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in par... more Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in particular proteins. One aspect that has been contentious is how much native solution-phase structure is preserved upon transposition to the gas phase by soft ionization methods such as electrospray ionization. To address this question-and thus further develop mass spectrometry as a tool for structural biology-structure-sensitive techniques must be developed to probe the gas-phase conformations of proteins. Here, we report Förster resonance energy transfer (FRET) measurements on a ubiquitin mutant using specific photofragmentation as a reporter of the FRET efficiency. The FRET data is interpreted in the context of circular dichroism, molecular dynamics simulation, and ion mobility data. Both the dependence of the FRET efficiency on the charge state-where a systematic decrease is observed-and on methanol concentration are considered. In the latter case, a decrease in FRET efficiency with met...
The Journal of Physical Chemistry Letters, 2016
Single-photon, two-electron photodetachment from nickel phthalocyanine tetrasulfonic acid tetra a... more Single-photon, two-electron photodetachment from nickel phthalocyanine tetrasulfonic acid tetra anions, NiPc 4-, was examined in the gas-phase using a linear ion trap coupled to the DESIRS VUV beamline of the SOLEIL Synchrotron. This system was chosen since it has a low detachment energy, known charge localization, and well defined geometrical and electronic structures. A threshold for two-electron loss is observed at 10.2 eV, around 1 eV lower than previously observed double detachment thresholds on multiple charged protein anions. The photodetachment energy of [NiPc] 4has been previously determined to be 3.5 eV and the photodetachment energy of [NiPc] 3-• is determined in this work to be 4.3 eV. The observed single photon double electron detachment threshold is hence 5.9 eV higher than the energy required for sequential single electron loss. Possible mechanisms are for double photodetachment are discussed. These observations pave the way toward new, exciting experiments for probing double photodetachment at relatively low energies, including correlation measurements on emitted photoelectrons.
Journal of the American Society for Mass Spectrometry, Sep 10, 2016
Herein we report the successful implementation of the consecutive and simultaneous photodissociat... more Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits...
Journal of the American Chemical Society, Jan 14, 2016
Charge transfer mechanisms lay at the heart of chemistry and biochemistry. Proton coupled electro... more Charge transfer mechanisms lay at the heart of chemistry and biochemistry. Proton coupled electron transfers (PCET) are central in biological processes such as photosynthesis and in the respiratory chain, where they mediate long range charge transfers. These mechanisms are normally difficult to harness experimentally due to the intrinsic complexity of the associated biological systems. Metal-peptide cations experience both electron and proton transfers upon photo-excitation, proving an amenable model system to study PCET. We report on a time-resolved experiment designed to follow this dual charge transfer kinetics in [HG3W+Ag](+) (H= histidine, G= glycine, W= tryptophan) on timescales ranging from femtoseconds to milliseconds. While electron transfer completes in less than 4 ps, it triggers a proton transfer lasting over hundreds of microseconds. Molecular dynamics simulations show that conformational dynamics play an important role in slowing down this reaction. This combined exper...
The Journal of Chemical Physics, 2015
Analytical chemistry, Jan 25, 2015
We investigated how the temperature and size of charged droplets are affected by the electrospray... more We investigated how the temperature and size of charged droplets are affected by the electrospray ionization (ESI) process, using in situ measurements involving laser-induced fluorescence and Mie scattering on a thermal gradient focusing ESI source. Rhodamine dyes were employed as temperature indicators using ratiometric intensity based fluorescence techniques. The results were compared to lifetime-based techniques using tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate, [Ru(bpy)3]2+). Both methods gave similar profiles. Nevertheless, the precision and sensitivity were higher for lifetime-based techniques in comparison to intensity-based techniques. Global warming (with ∆T ~10 K) of the ESI plume is reported while the size of the droplet decreases along the plume. The global warming indicates that the conductive thermal transfer (between the super-heated sheath gas and the solvent) is predominant and stronger than the cooling effect due to the evaporation of the droplets, an...
 (L = bis(diphenylphosphino)methane). A joint experimental and theoretical study](https://attachments.academia-assets.com/96536748/thumbnails/1.jpg)
](Physical chemistry chemical physics : PCCP, 2015
The bis(diphenylphosphino)methane (L = Ph2PCH2PPh2) ligated silver deuteride nanocluster dication... more The bis(diphenylphosphino)methane (L = Ph2PCH2PPh2) ligated silver deuteride nanocluster dication, [Ag10D8L6](2+), has been synthesised in the condensed phase via the reaction of bis(diphenylphosphino)methane, silver nitrate and sodium borodeuteride in the methanol : chloroform (1 : 1) mixed solvent system. The photoionisation and photofragmentation of this mass-selected cluster were studied using a linear ion trap coupled to the DESIRS VUV beamline of the SOLEIL Synchrotron. At 15.5 eV the main ionic products observed are [Ag10D8L5](2+), [Ag10D8L4](2+), [Ag10D8L6](3+)˙, [Ag9D8L4](2+)˙, and [AgL2](+). The later two products arise from fragmentation of [Ag10D8L6](3+)˙. An analysis of the yields of these product ions as a function of the photon energy reveals the onset for the formation of [AgL2](+) and [Ag9D8L4](2+)˙ is around 2 eV higher than that for ionisation to produce [Ag10D8L5](3+)˙. The onset of ionisation energy of [Ag10D8L6](2+) was determined to be 9.3 ± 0.3 eV from a fit ...
![Research paper thumbnail of Formation and Characterisation of the Silver Hydride Nanocluster Cation [Ag3H2((Ph2P)2CH2)]+and Its Release of Hydrogen](https://attachments.academia-assets.com/96536736/thumbnails/1.jpg)
](Chemistry - A European Journal, 2014
Multistage mass spectrometry and density functional theory (DFT) were used to characterise of the... more Multistage mass spectrometry and density functional theory (DFT) were used to characterise of the small silver hydride nanocluster, [Ag3H2L] + (where L = (Ph2P)2CH2) and its gas-phase unimolecular chemistry. Collision-induced dissociation (CID) yields [Ag2HL] + as the major product while laser-induced dissociation (LID) proceeds via H2 formation and subsequent release from [Ag3H2L] + , giving rise to [Ag3L] + as the major product. Deuterium labelling studies on [Ag3D2L] + prove that the source of H2 is from the hydrides and not from the ligand. Comparison of TDDFT absorption patterns obtained for the optimised structures with action spectroscopy results allows assignment of the measured features to structures of precursors and products. Molecular dynamics "on the fly" reveal that AgH loss is favoured in the ground state, but H2 formation and loss is preferred in the first excited state S1, in agreement with CID and LID experimental findings. This indicates favourable photo-induced formation of H2 and subsequent release from [Ag3H2L] + , an important finding in context of metal hydrides as a hydrogen storage medium, which can subsequently be released by heating or irradiation with light.
Journal of Pharmaceutical Analysis, 2014
Oral estrogens are directly associated with changes in plasma levels of coagulation proteins. Thu... more Oral estrogens are directly associated with changes in plasma levels of coagulation proteins. Thus, the detection of any variation in protein concentrations due to estrogen contraceptives, by a simultaneous analysis of both coagulation proteins and estrogens, would be a very informative tool. In the present study, the merit of photo-selected reaction monitoring (SRM), a new analytical tool, was evaluated towards estrogens detection in plasma. Then, SRM and photo-SRM detection modes were combined for the simultaneous analysis of estrogen molecules together with heparin co-factor and factor XIIa, two proteins involved in the coagulation cascade. This study shows that photo-SRM could open new multiplexed analytical routes.
The Analyst, 2014
Improvement of the fragmentation specificity may streamline data processing of bottom-up proteomi... more Improvement of the fragmentation specificity may streamline data processing of bottom-up proteomic experiments by drastically reducing either the amount of MS/MS data to process in the discovery phase or the detection of interfering signals in targeted quantification. Photodissociation at proper wavelengths is a promising alternative technique to the nondiscriminating conventional activation mode by collision. Here, we describe the implementation of visible LID at 473 nm in a Q-Exactive-Orbitrap mass spectrometer for the specific detection of cysteine-containing peptides tagged with a Dabcyl group. HCD cell DC offset and irradiation time were optimized to obtain high fragmentation yield and spectra free of contaminating CID product ions, while keeping the irradiation time scale compatible with chromatographic separation. With this optimized experimental setup , the selective detection of cysteine-containing peptides in a whole tryptic hydrolysate of three combined proteins is demonstrated by comparing all ion fragmentation (AIF) spectra recorded online with and without laser irradiation.
Physical Review Letters, 2000
The hypothesis that fullerenes grow in a carbon plasma by the addition of C 2 units (the "fullere... more The hypothesis that fullerenes grow in a carbon plasma by the addition of C 2 units (the "fullerene road") has been widely acclaimed as the most plausible mechanism for formation of larger fullerenes including C 60 and C 70. Calculations suggest that the association of C 2 with fullerenes proceeds through two classes of intermediates, "sticks" and "handles." Here we report the observation of these species using high-resolution ion-mobility measurements for C n cations generated by laser vaporization of graphite and laser desorption of C 60. Sticks with up to eight-atom chains have also been found.
Physical Review Letters, 1998
High-resolution ion-mobility measurements have resolved a number of isomers for carbon cluster an... more High-resolution ion-mobility measurements have resolved a number of isomers for carbon cluster anions in the drift-time region previously assigned to monocyclic rings. Tight-binding calculations have been performed to generate feasible geometries, which were compared to the experimental data by calculating their mobilities. Structures composed of a short chain of carbon atoms attached to a carbon ring are found to be the most plausible geometries for these new isomers. A number of different bicyclic ring isomers have also been resolved for the first time. [S0031-9007(98)06131-6]
Physical Review Letters, 1997
High resolution ion mobility measurements have been used to examine structural transitions in ͑Na... more High resolution ion mobility measurements have been used to examine structural transitions in ͑NaCl͒ n Cl 2 nanocrystals with between 30 and 40 NaCl units. Transformations between bulk fragment geometries with different j 3 k 3 l dimensions are observed at ambient temperatures. In some of these transformations, close to half the atoms are relocated, yet the Arrhenius activation energies are less than 0.6 eV. A surface diffusion mechanism is proposed to explain the remarkably low activation energies. [S0031-9007(97)03225-0]
Physical Review A, 2013
The laser-induced decay of ethylene oxide polymer ions of megadalton size has been studied in the... more The laser-induced decay of ethylene oxide polymer ions of megadalton size has been studied in the multiphoton IR excitation regime, with fragmentation products of individual ions being monitored over long times by a trapping device. The experiment reveals several fragmentation pathways having distinct signatures at the single-molecule level that would not be accessible from studies based on statistically averaged reaction rates only. The observations are supported by dedicated molecular simulations based on a coarse-grained model, which further highlight the role played by continuous heating in such out-of-equilibrium conditions. In particular, both experiment and modeling indicate that the dissociation kinetics depends nonlinearly on heating rate.
Physical Chemistry Chemical Physics, 2011
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of... more Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.
Structural Dynamics, 2020
A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a serie... more A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a series of poly-peptide radical cations containing both histidine and tryptophan. The proton transfer is driven by the gas-phase basicity difference between residues. The fragmentation scheme indicates that the gas-phase basicity of histidine is lower than that of radical tryptophan so that histidine is always pulling the proton away from tryptophan. However, the proton transfer requires the two basic sites to be in close proximity, which is rate limited by the peptide conformational dynamics. PT rate measurements were used to probe and explore the peptide conformational dynamics in several poly-glycines/prolines/alanines. For small and unstructured peptides, the PT rate decreases with the size, as expected from a statistical point of view in a flat conformational space. Conversely, if structured conformations are accessible, the structural flexibility of the peptide is decreased. This slows d...
Journal of the American Chemical Society, 2003
Amino acids exist as zwitterions in solution and in their canonical forms in the gas phase. 1-5 T... more Amino acids exist as zwitterions in solution and in their canonical forms in the gas phase. 1-5 The zwitterionic form can be stabilized in the gas phase by salt bridge interactions when a net charge is present, 6,7 or by shielding of the charges, either by the addition of water molecules 8,9 or by complex formation. 10 Calculations suggest that two water molecules are sufficient to stabilize a zwitterion in glycine, 11 the simplest amino acid. In peptides, the charge shielding function can be accomplished through self-solvation. At present, there is very little information available about the minimum peptide size required to stabilize a zwitterion, 12-14 and what information is available has been obtained on charged peptides using indirect methods. Here, we report studies of zwitterion formation in small neutral alanine-based peptides using, for the first time, a direct probe of the charge distribution. We have used molecular beam electric deflection measurements to determine the electric dipole susceptibility of unsolvated WA n and Ac-WA n-NH 2 (W) tryptophan and A) alanine) peptides with up to five alanines (the capped Ac-WA n-NH 2 peptides cannot form zwitterions). We find that the WA n peptides remain in the canonical form at room temperature. The measurements were performed on an apparatus consisting of a matrix-assisted laser desorption (MALD) source coupled to an electric beam deflection setup with a position-sensitive timeof-flight mass spectrometer. 15 The peptides were synthesized using FastMoc chemistry with an Applied Biosystems model 433A peptide synthesizer. MALD targets were prepared by pressing a 1:3 ratio of the peptide and high purity cellulose powder. Peptides were desorbed from the target with the third harmonic of a pulsed Nd:YAG laser (355 nm) into a helium flow generated with a piezoelectric valve that is synchronized with the desorption laser. A molecular beam leaves the source through a 5 cm long nozzle. Both ions and neutrals are produced in the desorption step. The ions are ejected from the beam with a transverse electric field, and the resulting neutral beam is tightly collimated by two slits before it travels through the 15 cm long electric deflector. The deflector provides both an electric field F (F) 0 to 2 × 10 7 V m-1) and a field gradient ∂F/∂z. The direction of the field, z, and its gradient are perpendicular to the beam axis. One meter after the deflector, the peptides are photoionized with the fourth harmonic of a Nd: YAG laser (266 nm) in the extraction region of a position-sensitive time-of-flight mass spectrometer. The velocity of the peptides in the neutral beam is selected and measured with a mechanical chopper that is synchronized with the ionization laser. The beam profile of rigid molecules is symmetrically broadened in the deflector, while for nonrigid molecules (i.e., when one cannot separate the vibrational and rotational Hamiltonians such as for those molecules studied here), the beam is globally deflected toward the high field. 16 The deflection:
The Journal of Physical Chemistry A, 2017
Journal of the American Society for Mass Spectrometry, 2018
The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage in... more The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are f...
Journal of the American Society for Mass Spectrometry, 2017
The visible photodissociation mechanisms of QSY7-tagged peptides of increasing size have been inv... more The visible photodissociation mechanisms of QSY7-tagged peptides of increasing size have been investigated by coupling a mass spectrometer and an optical parametric oscillator laser beam. The experiments herein consist of energy resolved collision-and laser-induced dissociation measurements on the chromophore-tagged peptides. The results show that fragmentation occurs by similar channels in both activation methods, but that the branching ratios are vastly different. Observation of a size-dependent minimum laser pulse energy required to induce fragmentation, and collisional cooling rates in time resolved experiments show that laser-induced dissociation occurs through the absorption of multiple photons by the chromophore and the subsequent heating through vibrational energy redistribution. The differences in branching ratio between collision-and laser-induced dissociation can then be understood by the highly anisotropic energy distribution following absorption of a photon.
Journal of the American Society for Mass Spectrometry, Jan 9, 2016
Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in par... more Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in particular proteins. One aspect that has been contentious is how much native solution-phase structure is preserved upon transposition to the gas phase by soft ionization methods such as electrospray ionization. To address this question-and thus further develop mass spectrometry as a tool for structural biology-structure-sensitive techniques must be developed to probe the gas-phase conformations of proteins. Here, we report Förster resonance energy transfer (FRET) measurements on a ubiquitin mutant using specific photofragmentation as a reporter of the FRET efficiency. The FRET data is interpreted in the context of circular dichroism, molecular dynamics simulation, and ion mobility data. Both the dependence of the FRET efficiency on the charge state-where a systematic decrease is observed-and on methanol concentration are considered. In the latter case, a decrease in FRET efficiency with met...
The Journal of Physical Chemistry Letters, 2016
Single-photon, two-electron photodetachment from nickel phthalocyanine tetrasulfonic acid tetra a... more Single-photon, two-electron photodetachment from nickel phthalocyanine tetrasulfonic acid tetra anions, NiPc 4-, was examined in the gas-phase using a linear ion trap coupled to the DESIRS VUV beamline of the SOLEIL Synchrotron. This system was chosen since it has a low detachment energy, known charge localization, and well defined geometrical and electronic structures. A threshold for two-electron loss is observed at 10.2 eV, around 1 eV lower than previously observed double detachment thresholds on multiple charged protein anions. The photodetachment energy of [NiPc] 4has been previously determined to be 3.5 eV and the photodetachment energy of [NiPc] 3-• is determined in this work to be 4.3 eV. The observed single photon double electron detachment threshold is hence 5.9 eV higher than the energy required for sequential single electron loss. Possible mechanisms are for double photodetachment are discussed. These observations pave the way toward new, exciting experiments for probing double photodetachment at relatively low energies, including correlation measurements on emitted photoelectrons.
Journal of the American Society for Mass Spectrometry, Sep 10, 2016
Herein we report the successful implementation of the consecutive and simultaneous photodissociat... more Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits...
Journal of the American Chemical Society, Jan 14, 2016
Charge transfer mechanisms lay at the heart of chemistry and biochemistry. Proton coupled electro... more Charge transfer mechanisms lay at the heart of chemistry and biochemistry. Proton coupled electron transfers (PCET) are central in biological processes such as photosynthesis and in the respiratory chain, where they mediate long range charge transfers. These mechanisms are normally difficult to harness experimentally due to the intrinsic complexity of the associated biological systems. Metal-peptide cations experience both electron and proton transfers upon photo-excitation, proving an amenable model system to study PCET. We report on a time-resolved experiment designed to follow this dual charge transfer kinetics in [HG3W+Ag](+) (H= histidine, G= glycine, W= tryptophan) on timescales ranging from femtoseconds to milliseconds. While electron transfer completes in less than 4 ps, it triggers a proton transfer lasting over hundreds of microseconds. Molecular dynamics simulations show that conformational dynamics play an important role in slowing down this reaction. This combined exper...
The Journal of Chemical Physics, 2015
Analytical chemistry, Jan 25, 2015
We investigated how the temperature and size of charged droplets are affected by the electrospray... more We investigated how the temperature and size of charged droplets are affected by the electrospray ionization (ESI) process, using in situ measurements involving laser-induced fluorescence and Mie scattering on a thermal gradient focusing ESI source. Rhodamine dyes were employed as temperature indicators using ratiometric intensity based fluorescence techniques. The results were compared to lifetime-based techniques using tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate, [Ru(bpy)3]2+). Both methods gave similar profiles. Nevertheless, the precision and sensitivity were higher for lifetime-based techniques in comparison to intensity-based techniques. Global warming (with ∆T ~10 K) of the ESI plume is reported while the size of the droplet decreases along the plume. The global warming indicates that the conductive thermal transfer (between the super-heated sheath gas and the solvent) is predominant and stronger than the cooling effect due to the evaporation of the droplets, an...
Physical chemistry chemical physics : PCCP, 2015
The bis(diphenylphosphino)methane (L = Ph2PCH2PPh2) ligated silver deuteride nanocluster dication... more The bis(diphenylphosphino)methane (L = Ph2PCH2PPh2) ligated silver deuteride nanocluster dication, [Ag10D8L6](2+), has been synthesised in the condensed phase via the reaction of bis(diphenylphosphino)methane, silver nitrate and sodium borodeuteride in the methanol : chloroform (1 : 1) mixed solvent system. The photoionisation and photofragmentation of this mass-selected cluster were studied using a linear ion trap coupled to the DESIRS VUV beamline of the SOLEIL Synchrotron. At 15.5 eV the main ionic products observed are [Ag10D8L5](2+), [Ag10D8L4](2+), [Ag10D8L6](3+)˙, [Ag9D8L4](2+)˙, and [AgL2](+). The later two products arise from fragmentation of [Ag10D8L6](3+)˙. An analysis of the yields of these product ions as a function of the photon energy reveals the onset for the formation of [AgL2](+) and [Ag9D8L4](2+)˙ is around 2 eV higher than that for ionisation to produce [Ag10D8L5](3+)˙. The onset of ionisation energy of [Ag10D8L6](2+) was determined to be 9.3 ± 0.3 eV from a fit ...
Chemistry - A European Journal, 2014
Multistage mass spectrometry and density functional theory (DFT) were used to characterise of the... more Multistage mass spectrometry and density functional theory (DFT) were used to characterise of the small silver hydride nanocluster, [Ag3H2L] + (where L = (Ph2P)2CH2) and its gas-phase unimolecular chemistry. Collision-induced dissociation (CID) yields [Ag2HL] + as the major product while laser-induced dissociation (LID) proceeds via H2 formation and subsequent release from [Ag3H2L] + , giving rise to [Ag3L] + as the major product. Deuterium labelling studies on [Ag3D2L] + prove that the source of H2 is from the hydrides and not from the ligand. Comparison of TDDFT absorption patterns obtained for the optimised structures with action spectroscopy results allows assignment of the measured features to structures of precursors and products. Molecular dynamics "on the fly" reveal that AgH loss is favoured in the ground state, but H2 formation and loss is preferred in the first excited state S1, in agreement with CID and LID experimental findings. This indicates favourable photo-induced formation of H2 and subsequent release from [Ag3H2L] + , an important finding in context of metal hydrides as a hydrogen storage medium, which can subsequently be released by heating or irradiation with light.
Journal of Pharmaceutical Analysis, 2014
Oral estrogens are directly associated with changes in plasma levels of coagulation proteins. Thu... more Oral estrogens are directly associated with changes in plasma levels of coagulation proteins. Thus, the detection of any variation in protein concentrations due to estrogen contraceptives, by a simultaneous analysis of both coagulation proteins and estrogens, would be a very informative tool. In the present study, the merit of photo-selected reaction monitoring (SRM), a new analytical tool, was evaluated towards estrogens detection in plasma. Then, SRM and photo-SRM detection modes were combined for the simultaneous analysis of estrogen molecules together with heparin co-factor and factor XIIa, two proteins involved in the coagulation cascade. This study shows that photo-SRM could open new multiplexed analytical routes.
The Analyst, 2014
Improvement of the fragmentation specificity may streamline data processing of bottom-up proteomi... more Improvement of the fragmentation specificity may streamline data processing of bottom-up proteomic experiments by drastically reducing either the amount of MS/MS data to process in the discovery phase or the detection of interfering signals in targeted quantification. Photodissociation at proper wavelengths is a promising alternative technique to the nondiscriminating conventional activation mode by collision. Here, we describe the implementation of visible LID at 473 nm in a Q-Exactive-Orbitrap mass spectrometer for the specific detection of cysteine-containing peptides tagged with a Dabcyl group. HCD cell DC offset and irradiation time were optimized to obtain high fragmentation yield and spectra free of contaminating CID product ions, while keeping the irradiation time scale compatible with chromatographic separation. With this optimized experimental setup , the selective detection of cysteine-containing peptides in a whole tryptic hydrolysate of three combined proteins is demonstrated by comparing all ion fragmentation (AIF) spectra recorded online with and without laser irradiation.
Physical Review Letters, 2000
The hypothesis that fullerenes grow in a carbon plasma by the addition of C 2 units (the "fullere... more The hypothesis that fullerenes grow in a carbon plasma by the addition of C 2 units (the "fullerene road") has been widely acclaimed as the most plausible mechanism for formation of larger fullerenes including C 60 and C 70. Calculations suggest that the association of C 2 with fullerenes proceeds through two classes of intermediates, "sticks" and "handles." Here we report the observation of these species using high-resolution ion-mobility measurements for C n cations generated by laser vaporization of graphite and laser desorption of C 60. Sticks with up to eight-atom chains have also been found.
Physical Review Letters, 1998
High-resolution ion-mobility measurements have resolved a number of isomers for carbon cluster an... more High-resolution ion-mobility measurements have resolved a number of isomers for carbon cluster anions in the drift-time region previously assigned to monocyclic rings. Tight-binding calculations have been performed to generate feasible geometries, which were compared to the experimental data by calculating their mobilities. Structures composed of a short chain of carbon atoms attached to a carbon ring are found to be the most plausible geometries for these new isomers. A number of different bicyclic ring isomers have also been resolved for the first time. [S0031-9007(98)06131-6]
Physical Review Letters, 1997
High resolution ion mobility measurements have been used to examine structural transitions in ͑Na... more High resolution ion mobility measurements have been used to examine structural transitions in ͑NaCl͒ n Cl 2 nanocrystals with between 30 and 40 NaCl units. Transformations between bulk fragment geometries with different j 3 k 3 l dimensions are observed at ambient temperatures. In some of these transformations, close to half the atoms are relocated, yet the Arrhenius activation energies are less than 0.6 eV. A surface diffusion mechanism is proposed to explain the remarkably low activation energies. [S0031-9007(97)03225-0]
Physical Review A, 2013
The laser-induced decay of ethylene oxide polymer ions of megadalton size has been studied in the... more The laser-induced decay of ethylene oxide polymer ions of megadalton size has been studied in the multiphoton IR excitation regime, with fragmentation products of individual ions being monitored over long times by a trapping device. The experiment reveals several fragmentation pathways having distinct signatures at the single-molecule level that would not be accessible from studies based on statistically averaged reaction rates only. The observations are supported by dedicated molecular simulations based on a coarse-grained model, which further highlight the role played by continuous heating in such out-of-equilibrium conditions. In particular, both experiment and modeling indicate that the dissociation kinetics depends nonlinearly on heating rate.
Physical Chemistry Chemical Physics, 2011
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of... more Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.